"There are people who have been in this investigation from the beginning who believe that before they even started the investigation, that they had decided it was Lee," says Vrooman, former head of counterintelligence at Los Alamos.
The investigators drew up a list of 70 suspects that included Lee. Then, they narrowed the list to 12.
"It appeared to me like it was a bogus list, to give the appearance of doing a legitimate investigation," Vrooman says. "There's one person on there who doesn't have a clearance. There are other people on there who don't have access to nuclear weapons information. The investigators just told me, 'Well, look, I know it's Lee and ah, we just need some other names to make this thing look good.'"
Notra Trulock is the man credited with pushing the theory of Lee as the prime suspect from the very beginning. As the former head of Energy department counterintelligence, he headed the department's spy search. "I don't believe there was any preconceived notion about Lee," Trulock insists. "I have confidence in the investigation and the investigators that compiled that list."
But Vrooman isn't the first person to question the government's investigation of Lee. Lee remained the FBI's prime suspect even after field agents had cleared him and sent a memo to headquarters saying he was not their man.
Also, as CBS News reported two weeks ago, three Energy department polygraphers gave Lee passing scores on a lie detector test. The FBI reviewed the results and said Lee had actually failed the test
The FBI and Energy department point out that the inconsistencies don't mean Lee is innocent, and even though he was never charged with espionage, Lee's trial for alleged computer and security violations will provide more insight into how he became their chief spy suspect.